TDWG (Firenze 2013) Description of the ViBRANT project. 30th Oct 2013

1. ViBRANT
Virtual Biodiversity
ViBRANT: progress towards an
integrated framework
Vince Smith & Dave Roberts
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

2. ViBRANT
Virtual Biodiversity
ViBRANTs contribution
17 partners in 9 countries
(universities, museums & SMEs)
Interoperability, workflows, services, information modeling & user support
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

3. ViBRANT
Virtual Biodiversity
Training
& outreach
Support
services
ViBRANT Goals
Vision
Connecting the people, data & science of
biodiversity
http://vbrant.eu
SEVENTH FRAMEWORK
PROGRAMME
Controlled
vocabulary
Networking
Training
Standards
Mobilisation
Sociology
Data
aggregation
Field
recording
GBIF
integration
Citizen
science
Position
Open & sustainable development of a
federated network of biodiversity
informatics infrastructures
Mission
Facilitate the mobalisation, sharing,
reuse and publication of biodiversity data
Data
standards
Visualisation
Scratchpads
Virtual Research
Environment
Scratchpad
Phylogeny
tools
hosting
Bioclimatic
modelling
Software integration
Identification
tools
Matrix data
editor
Data
publishing
Service
Data
Publishing
Manuscript
publishing
Sustainability
Communal
literature
Research
Literature
mark up
Architecture
Literature
Data mining
-infrastructure

4. ViBRANT
Virtual Biodiversity
ViBRANT Outputs
E-Infrastructure
•
•
•
•
•
•
A Virtual Research Environment (Scratchpads) where users can safely store, share and
manage data.
Analytical services for users to build identification keys and phylogenetic trees.
A publication platform for users to automatically compile manuscripts from their research
database.
A portal for users to centrally access publicly accessible biodiversity research
information and literature.
Training, support & sociological study, helping research communities to use these tools
and services.
A standards compliant technical architecture that can be sustained by biodiversity
research community.
Products (extra-network activities because of the infrastructure)
•
•
•
Content: eBooks, eJournals, Con. assessments, flora and faunal studies, long term
data repositories, community vocabulariers, id. guides, citizen science projects.
Code: Drupal modules, OBOE services
New sectors of interest: agriculture, education
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

5. ViBRANT
Virtual Biodiversity
Knowledge Organization System
GBIF Service migrated to GBIF Secretariat (hosting)
TDWD VoMaG task group installed (governance)
Species-ID Semantic Media Wiki Integrated with GBIF-KOS system
Scratchpad Common Access point
CDM <–> Scratchpad and CDM <–> Xper2 pipelines
Pipelines further defined via DwC-A extensions & SDD
Improved data interfaces & API
New vocabularies supported (e.g. Audubon Core)
Development of APIs on the CDM
Liaise with major initiatives
TDWG, EOL, EU-BON, & LifeWatch
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

6. ViBRANT
Virtual Biodiversity
200
180
160
Users
140
120
100
80
60
40
20
0
2011
2012
2013
1000
900
800
Tasks
700
600
500
400
300
200
100
Oxford Batch Operations Engine
SEVENTH FRAMEWORK
PROGRAMME
0
https://oboe.oerc.ox.ac.uk/
-infrastructure

7. ViBRANT
Virtual Biodiversity
http://biblife.org
RefBank nodes
http://zoobank.org/RefBank
more nodes coming soon ....
Currently holds about
210,000 references
Citations growing at
about 5,000 / month
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

8. ViBRANT
Virtual Biodiversity
Number of Citations
Papers mentioning a Scratchpad Site
90
80
70
60
10000
8000
50
40
10
0
2008
2009
2010
Number of Citations
2011
600
2012
400
300
Papers mentioning the Scratchpad Project
Sites
25
20
6000
5000
4000
Sites
Users
Active Users
20
3000
2000
200
1000
100
15
10
50
5
30
0
2008
SEVENTH FRAMEWORK
PROGRAMME
2009
2010
2011
2012
Users
30
500
2007
2008
2009
2010
ViBRANT
2011
2012
2013
Scratchpads 2
-infrastructure

9. ViBRANT
Virtual Biodiversity
irtual
http://www.comber.hcmr.gr
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

10. ViBRANT
The target audience:
Nodes that have limited web presence.
Virtual Biodiversity
The approach:
Using the country checklist generated from the
GBIF mediated data to dynamically retrieve
biodiversity information from GBIF & EOL.
The result:
A web portal that is easy to set up,
customise, and enables joint development.
An example site at http://nptstartup.gbif.org
The code is available at
https://git.scratchpads.eu/git/scratchpads-2.0.git
as a branch “gbif-npt-startup”
Import the checklist requested separately by writing
to nodes@gbif.org
http://links.gbif.org/npt
Finish the setup with initial news and textual contents
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

11. ViBRANT
Virtual Biodiversity
PWT or Scratchpads
About Pensoft
Books
E-Books
Journals
News & Blog
Register | Login
Contact
Start a manuscript
All
Author
Title
How it works
Articles
About
Journal features
1. Define the
publication
Resolving the publishing
bottleneck for
biodiversity
Focus and Scope
Globally unique innovations
Criteria for publication
Peer review
For authors
Data publication
Science is a combination of gathering
facts and making theories; neither can
progress on its own. In the history of
science, the laborious accumulation of
facts is the dominant mode, not a
novelty.
Publication fees
Licenses and Copyright
Frequently Asked Questions
(FAQ)
Contacts
Editorial team
Most visited papers
This work is licensed under the
Creative Commons Attribution 3.0
(CC-BY).
Making “small” data big
No lower/upper limit of
manuscript size
Publish all kinds of biodiversity
related data
Reduced page charges
affordable by all
More than just data
journal!
Integrated text and data
publishing
Completely online revisions and
editing
Community ownership of data
Community peer-review
3 days from acceptance to
publication
Public peer-review on author’s
choice
Why publish my data?
Increase collaboration
Re-use and multiply effect
Taxon
treatments
Plazi
Establish scientific priority
Link data to a bigger
network
4. Organise
manuscript
Citable publication
Occurrence
7 weeks from submission to
decision
Free of charge in launch phase
3. Select taxa
& content
Bibliographies
Peter Norvig
Follow us
2. Enter
metadata
Articles
Respond to funding
requirements
Editor-in-Chief: VINCENT SMITH
Natural History Museum, London, UK
Taxon
names
5. Submit to
journal
I . P . N . I
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure

12. ViBRANT
Virtual Biodiversity
Be
agile
Users
need
Lessons
Have a Champion
Deliver an
immediate benefit to users
Market your products!!!
SEVENTH FRAMEWORK
PROGRAMME
-infrastructure